Why aren't bpy.props defined on the WindowManager saved on permanently?
The window-manager is an exception when it comes to data-blocks, having some characteristics that make it work differently then meshes, scenes... etc.


Can't be added or removed.
Its a singleton (there is only ever one).
Its not saved in the blend file (this is why properties aren't set on reload).


This can be handy, for example - this is used for the add-on and key-map search text fields.

For persistent data, its normally best to use...


the current scene (context.scene).
add-on-preferences
in a sub-directory of user resources (as json/xml/pickled data... etc).